Unlocking the Potential of Rice for Thermotolerance using SSR Marker- Based Assessment of Genetic Variability and Population Structure

Abstract

Abstract Climate change due to global warming is causing an increase in heat stress in rice (Oryza sativa L.). Heat stress reduces the yield of rice, which is one of the major staple crop for half of the world's population. Therefore, there is a dire need to breed heat-tolerant rice cultivars. In any crop improvement program, the presence of genetic diversity and evaluation of the structural association are crucial for developing the breeding strategies. This study was conducted to examine the genetic variability and population structure of 49 rice genotypes, including both released rice varieties and advanced breeding lines using 75 SSR markers linked to thermotolerance located across the 12 rice chromosomes. A total of 113 alleles, with the number of alleles ranging from 2 to 4 and a mean of 2.31 alleles per locus. The average values for polymorphic information content (PIC), genetic diversity and major allele frequency were 0.36, 0.35 and 0.71 respectively. Among the markers evaluated, RM4108 exhibited highest PIC value (0.65) and gene diversity (0.64), indicating that it is highly polymorphic marker and an ideal choice for characterizing Thermotolerance rice cultivars. Both genetic distance-based clustering analysis and population structure revealed that the 49 cultivars formed three significant clusters. Cluster 1 comprised a mixture of 7 released varieties and 12 breeding lines, followed by cluster 2, which included 11 released varieties and 8 breeding lines. Cluster 3 consisted a total of 11 released varieties. Furthermore, the principal coordinate analysis demonstrated cumulative genetic variations of 15.60%, 14.17%, 8.03% and 7.02% among the mixed populations. Most of the released varieties were placed in coordinate 1, while breeding lines were found in coordinate 3. The analysis of Maruteru rice cultivars revealed a diverse genetic composition and the obtained information will be valuable for establishing an association panel and selecting suitable parents for future rice development programs.